Abstract 997: Cell-free DNA fragmentomics distinguish between benign, pre-malignant and malignant peripheral nerve sheath tumors in neurofibromatosis type 1
Authors: Alex C. Pan, Russell Taylor Sundby, Jeffrey J. Szymanski, Paul A. Jones, Peter K. Harris, Aadel A. Chaudhuri, Angela C. Hirbe, Jack F. Shern
Journal: Cancer Research (2023)

Abstract Background: Malignant peripheral nerve sheath tumors (MPNST) are aggressive soft tissue sarcomas that, in the setting of neurofibromatosis type 1 (NF1), arise within pre-malignant atypical neurofibroma (AN) and benign plexiform neurofibroma (PN). Early surgical resection improves prognosis, however, early detection by imaging and tissue biopsies is challenging due to tissue heterogeneity. In this multi-institutional study we analyze fragmentomic profiles of plasma cell free DNA (cfDNA) to non-invasively distinguish between NF1 associated PN, AN and MPNST. Accurate classification would inform clinical care: standards of care for PN is observation, AN is narrow-margin resection, and MPNST is wide-margin resection. Methods: We performed whole genome sequencing of plasma cfDNA samples from healthy controls (n = 21), patients with PN (n = 113), AN (n = 39) and MPNST (n = 71). cfDNA fragment profiles were analyzed using two complementary approaches. First, we used unsupervised non-negative matrix factorization (NMF) to obtain global fragment length signatures to infer tumor fragment length distributions. The optimal cutpoint was determined after receiver operating characteristic analysis by Youden’s index in one-versus-one (OVO) disease state comparisons. Additionally, we implemented a bin-wise fragmentomic analysis based on DELFI, training a classifier on the ratios of short (100-150bp) and long (151-220bp) fragments in 5 megabase regions across the genome and arm-level features. Results: NMF accurately distinguished disease states on OVO comparisons: MPNST v AN (acc 0.71), MPNST v PN (acc 0.75), MPNST v healthy (acc 0.84), AN v PN (acc 0.70), AN v healthy (acc 0.80) and PN v healthy (acc 0.87). Accuracies were moderately improved in nearly all conditions with bin-wise fragmentomics: MPNST v AN (acc 0.62), MPNST v PN (acc 0.83), MPNST vs healthy (acc 0.86), AN v PN (acc 0.87), AN vs healthy (acc 0.72) and PN vs healthy (acc 0.88). Strikingly, the two AN with the DELFI scores most closely resembling MPNST were separately identified by independent clinical care teams to have very high-risk features and recent history warranting short-interval follow up. Conclusions: This study demonstrates that the spectrum of benign, pre-malignant and malignant peripheral nerve sheath tumors have distinct, disease state specific fragmentomic signatures. Fragmentomics alone outperformed our previously published copy number based cfDNA classifier in all conditions, most notably in low mutational burden healthy, PN and AN states. Finally, preliminary clinical vignettes suggest that this approach may be able to inform surveillance intervals by identifying higher risk premalignant lesions. Together, this work has the potential to enable earlier detection of clinically actionable AN and early-stage MPNST, thereby improving survival outcomes. Citation Format: Alex C. Pan, Russell Taylor Sundby, Jeffrey J. Szymanski, Paul A. Jones, Peter K. Harris, Aadel A. Chaudhuri, Angela C. Hirbe, Jack F. Shern. Cell-free DNA fragmentomics distinguish between benign, pre-malignant and malignant peripheral nerve sheath tumors in neurofibromatosis type 1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 997.